I. Retroviruses
The Retroviridae virus family encompasses all viruses containing an RNA genome and producing an RNA-dependent DNA polymerase (reverse transcriptase). The family is divided into three subfamilies: (1) Oncovirinae, including all the oncogenic retroviruses (referred to in the older literature as "oncornaviruses") and several closely related nononcogenic viruses (collectively referred to herein as "oncoretroviruses"); (2) Lentivirinae, the "slow retroviruses," such as the human immunodeficiency virus (HIV) and visna virus; and (3) Spumavirinae, the "foamy" retroviruses that induce persistent infections, generally without causing any clinical disease. More detailed descriptions of the retroviruses may be found in Weiss et al., (eds), RNA Tumor Viruses, Cold Spring Harbor Laboratory, N.Y., 1985; Doolittle, et al., Quart. Rev. Biol., 64:1-29, 1979; and Varmus and Brown, Retroviruses, p. 53-108, in Berg and Howe, (eds), 1989, Mobile DNA, American Society for Microbiology, Washington, D.C.
In broadest overview, the life cycle of a retrovirus comprises entry of an infectious retroviral particle into a host cell, integration of the virus' genetic information into the host cell's genome, and production of new infectious retroviral particles by the biosynthetic machinery of the infected host cell. More specifically, upon entering a cell, a retroviral particle initiates a series of interactive biochemical steps that results in the production of a DNA copy of the virus' RNA genome and its integration into the nuclear DNA of the cell. This integrated DNA copy is referred to as a provirus and can be inherited by any daughter cells of the infected cell like any other gene. See Goff, Annu. Rev. Genet., 26:527-544, 1992.
All retroviral particles share common morphological, biochemical, and physical properties, including:
(1) A linear, positive-sense, single-stranded RNA genome composed of two identical subunits and making up about 1% of the mass of the virus.
(2) At least three types of proteins encoded by the viral genome, i.e., gag proteins (the group antigen internal structural proteins), pol proteins (the RNA-dependent DNA polymerase and the protease and integrase proteins), and env proteins (the viral envelope protein or proteins). These proteins together make up about 60%-70% of the mass of the virus.
(3) Lipid derived from the cell membrane of an infected cell making up about 30%-40% of the mass of the virus.
(4) Carbohydrate associated with the env proteins, making up about 2-4% of the mass of the virus.
(5) An overall spherical morphology with variable surface projections.
(6) An isocahedral capsid structure containing a ribonucleoprotein complex within an internal nucleoid or nucleocapsid shell.
In addition to genes encoding the gag, pol, and env proteins, the genome of the retrovirus includes two long terminal repeat (LTR) sequences, one at each end of the linear genome. These 5' and 3' LTRs serve to promote transcription and polyadenylation of viral mRNAs and participate in the integration of the viral genome into the genomic DNA of the infected host cell. Adjacent to the 5' LTR are sequences necessary for reverse transcription of the viral genome (the tRNA primer binding site) and the .psi. site, a sequence that directs the encapsulation of viral RNA into retroviral particles (virions). See Mulligan, In: Experimental Manipulation of Gene Expression, Inouye (ed), 155-173, 1983; Mann, et al., Cell, 33:153-159, 1983; Cone, and Mulligan, Proceedings of the National Academy of Sciences, U.S.A., 81:6349-6353, 1984.
The protein products encoded by the gag, pol, and env genes are generally synthesized by the infected cell as polyproteins that are subsequently cleaved to produce the final separate protein products. In particular, the translation products of the oncoretroviral gag genes are generally produced as a 60-80 kDa polyprotein translation product that is subsequently cleaved to form at least three gag proteins, including the matrix (MA), capsid (CA) and nucleocapsid (NC) proteins.
The gag proteins of specific oncoretroviruses are often referred to in the art by the prefix p followed by a number representing their approximate molecular weight in kilodaltons. For example, the four gag proteins of the Moloney murine leukemia virus (MoMLV) are referred to as p10 (NC), p12, p15 (MA), and p30 (CA).
The gag matrix and capsid proteins have multiple functions. Late in infection, after integration of the viral genetic material into the host cell genome, they both play essential roles by contributing to the structure of nascent viral particles. Earlier in infection, they participate in the transfer of the DNA copy of the virus' genome into the host cell's genome. They carry out this function as part of nucleoprotein structures referred to in the art as "nucleoprotein complexes" or "preintegration complexes." These complexes assemble in the host cell's cytoplasm and comprise the DNA copy of the virus' genome, the viral integrase protein, and either or both of the MA and CA proteins. See Bowerman et al., Genes & Development, 3:469-478, 1989; Bukrinsky, et al., Proc. Natl. Acad. Sci. USA, 89:6580-6584, 1992; and Bukrinsky, et al., Proc. Natl. Acad. Sci. USA, 90:6125-6129, 1993.